library(dplyr)
library(ggplot2)
library(DESeq2)
library(tximport)
library(readr)
library(tximportData)
library(readxl)
library(knitr)
library(tidyverse)
library(pheatmap)
library(RColorBrewer)
library(viridis)
library(ggrepel)
library(EnhancedVolcano)
library(fgsea)
library(limma)
Plasma 1:10
Viridis 1:10
Cividis 1:10
Magma 1:10
| Sample | patient | reads | %Q30 | Duplication rate | % reads with adapter | STAR alignment number | percent aligned | splices annotated | salmon mapping |
|---|---|---|---|---|---|---|---|---|---|
| Bulk | HTB314 | 71816976 | 94.3 | 57 | 2.6 | 63614504 | 88.58 | 27340654 | 85.6967 |
| Bulk | MDS268 | 31441538 | 93.0 | 24 | 2.3 | 25549835 | 81.26 | 5546270 | 58.2075 |
| Bulk | MDS280 | 28794421 | 93.0 | 24 | 2.3 | 23317205 | 80.98 | 5115546 | 58.8614 |
| CD123+ | HTB314 | 61568500 | 94.0 | 56 | 2.7 | 55359277 | 89.91 | 22831187 | 86.4197 |
| CD123+ | MDS268 | 32307881 | 93.0 | 27 | 3.3 | 26243441 | 81.23 | 7290861 | 64.2150 |
| CD123+ | MDS280 | 23745205 | 93.0 | 34 | 2.6 | 21035358 | 88.59 | 5668653 | 71.3245 |
| CD123- | HTB314 | 83260626 | 94.0 | 58 | 2.6 | 74804722 | 89.84 | 31876605 | 87.6505 |
| CD123- | MDS268 | 27917999 | 93.0 | 26 | 2.7 | 22835189 | 81.79 | 5793322 | 63.9284 |
| CD123- | MDS280 | 24767573 | 93.0 | 32 | 2.6 | 22467937 | 90.72 | 4773823 | 62.7193 |
## PCA plot
## 3. Run Differential Expression testing using DESeq2 and Calculate Gene Set Enrichment ## Compare 123pos vs 123neg, 123neg vs bulk, and 123pos vs bulk #### sig = padj <0.01 and abs(l2fc) >0.5 ####
## [1] TRUE
## [1] FALSE
## [1] TRUE
## [1] 1405
## [1] 2382
## [1] 2336
## [1] 1206
## [1] 2157
## [1] 2130
## [1] 939
## [1] 1112
###MA plots